PDB-4yan: Crystal structure of LigE in complex with glutathione (GSH) from ...

ID or keywords:

Entry

Database: PDB / ID: 4yan

Title

Crystal structure of LigE in complex with glutathione (GSH) from Sphingobium sp. strain SYK-6

Components

Beta-etherase

Keywords

TRANSFERASE / Glutathione-S-transferase B-etherase

Function / homology

Function and homology information

: / : / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase, N-terminal domain / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology

Biological species

Sphingobium sp. SYK-6 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.593 Å

Authors

Pereira, J.H. / McAndrew, R.P. / Heins, R.A. / Sale, K.L. / Simmons, B.A. / Adams, P.D.

Citation

Journal: J.Biol.Chem. / Year: 2016
Title: Structural Basis of Stereospecificity in the Bacterial Enzymatic Cleavage of beta-Aryl Ether Bonds in Lignin.
Authors: Helmich, K.E. / Pereira, J.H. / Gall, D.L. / Heins, R.A. / McAndrew, R.P. / Bingman, C. / Deng, K. / Holland, K.C. / Noguera, D.R. / Simmons, B.A. / Sale, K.L. / Ralph, J. / Donohue, T.J. / ...

History

Deposition	Feb 17, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 16, 2015	Provider: repository / Type: Initial release
Revision 1.1	Mar 16, 2016	Group: Database references
Revision 1.2	Jul 20, 2016	Group: Data collection
Revision 1.3	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4yan.cif.gz	585 KB	Display	PDBx/mmCIF format
PDB format	pdb4yan.ent.gz	497.8 KB	Display	PDB format
PDBx/mmJSON format	4yan.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4yan_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	4yan_full_validation.pdf.gz	1.5 MB	Display
Data in XML	4yan_validation.xml.gz	38.1 KB	Display
Data in CIF	4yan_validation.cif.gz	50.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ya/4yan ftp://data.pdbj.org/pub/pdb/validation_reports/ya/4yan	HTTPS FTP

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Related structure data

Related structure data	4xt0C 4yamC 4y98 4y9d 4ya6 4yac 4yae 4yag 4yai 4yap 4yav C: citing same article (ref.)
Similar structure data	4yam-1 4pgc-2 1moe-d 4yam-2 1goz-d 3rpi-2 3rgv-3 3adu-2 5pxc-d 6e5a-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#212 - Aug 2017 Glutathione Transferases similarity (5) #255 - Mar 2021 Cisplatin and DNA similarity (4)

Deposited unit

A: Beta-etherase

B: Beta-etherase

C: Beta-etherase

D: Beta-etherase

hetero molecules

130 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Beta-etherase

B: Beta-etherase

hetero molecules

defined by author&software
64.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Beta-etherase

D: Beta-etherase

hetero molecules

defined by author&software
64.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	121.006, 96.137, 126.164
Angle α, β, γ (deg.)	90.00, 81.52, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Beta-etherase Mass: 32106.279 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphingobium sp. SYK-6 (bacteria) / Gene: ligE, SLG_08660 / Production host: Escherichia coli (E. coli) / References: UniProt: G2IN93
#2: Chemical	ChemComp-GSH / GLUTATHIONE Mass: 307.323 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₃O₆S
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.83 Å³/Da / Density % sol: 56.47 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 M Ammonium Citrate, 0.1 M MES pH 5.5, 20% PEG 3,350, 5% Isopropanol PH range: 5.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.00002 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 14, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.00002 Å / Relative weight: 1
Reflection	Resolution: 2.593→50 Å / Num. obs: 42163 / % possible obs: 97.7 % / Redundancy: 3.8 % / Net I/σ(I): 6.1

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: dev_1839)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Resolution: 2.593→50 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.07 / Phase error: 25.9 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2671	2000	4.74 %
R_work	0.2229	-	-
obs	0.225	42158	94.81 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.593→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8246	0	80	165	8491

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	8588
X-RAY DIFFRACTION	f_angle_d	0.776	11707
X-RAY DIFFRACTION	f_dihedral_angle_d	12.704	3155
X-RAY DIFFRACTION	f_chiral_restr	0.03	1197
X-RAY DIFFRACTION	f_plane_restr	0.003	1536

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.5934-2.6582	0.2908	126	0.266	2526	X-RAY DIFFRACTION	84
2.6582-2.7301	0.2916	144	0.2621	2890	X-RAY DIFFRACTION	97
2.7301-2.8104	0.2945	144	0.2518	2912	X-RAY DIFFRACTION	97
2.8104-2.9011	0.3029	145	0.2452	2883	X-RAY DIFFRACTION	96
2.9011-3.0048	0.2913	145	0.2413	2918	X-RAY DIFFRACTION	96
3.0048-3.1251	0.3099	143	0.2358	2863	X-RAY DIFFRACTION	96
3.1251-3.2672	0.2476	142	0.2351	2852	X-RAY DIFFRACTION	95
3.2672-3.4395	0.2977	143	0.2249	2879	X-RAY DIFFRACTION	94
3.4395-3.6549	0.2461	140	0.209	2832	X-RAY DIFFRACTION	94
3.6549-3.937	0.257	139	0.2134	2785	X-RAY DIFFRACTION	92
3.937-4.3329	0.251	140	0.2011	2805	X-RAY DIFFRACTION	92
4.3329-4.9593	0.2574	144	0.199	2883	X-RAY DIFFRACTION	95
4.9593-6.2461	0.2467	151	0.2159	3022	X-RAY DIFFRACTION	99
6.2461-48.0769	0.248	154	0.2162	3108	X-RAY DIFFRACTION	100

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	1.2302	-0.2677	0.5059	0.7115	-0.2248	1.6444	0.0257	0.0694	-0.1679	-0.411	-0.0486	0.3058	0.131	-0.1888	0.0694	0.3492	-0.0281	-0.1194	0.2131	-0.0159	0.3819	-19.0934	48.2196	10.1559
2	1.2546	-0.7917	0.4061	2.6308	0.32	2.5722	0.1866	0.0476	0.054	-0.1999	-0.1115	0.0934	-0.1719	-0.2017	-0.0494	0.2455	-0.0204	-0.0415	0.1735	0.0502	0.2427	-13.6487	61.5029	19.7263
3	2.976	1.0934	0.5023	2.0766	0.2742	4.0763	0.0142	-0.1608	-0.1245	0.3241	-0.1081	0.1962	0.3469	0.1806	0.0622	0.2114	0.0171	-0.0046	0.1419	-0.0187	0.2208	11.8649	33.8018	40.5741
4	4.8583	0.9092	1.9543	1.938	0.4662	4.8877	0.2144	0.1445	0.2357	-0.0882	-0.266	-0.3956	-0.1194	0.311	0.0019	0.1472	-0.01	0.0244	0.1907	0.0385	0.3731	14.3243	37.3479	29.8705
5	0.7174	-0.4411	0.8264	0.5122	-0.204	1.3046	0.0046	-0.0163	0.1367	0.002	-0.1505	-0.0592	0.1246	0.2043	0.127	0.1678	-0.0339	0.0049	0.1856	-0.0155	0.314	-0.5101	45.3016	41.8956
6	7.5923	-1.6722	-0.3032	2.3387	-0.2346	0.9337	-0.7958	-0.0744	0.8196	0.1822	0.2511	-0.5052	-0.0314	-0.2559	0.2875	0.3664	0.016	-0.0724	0.2494	-0.0707	0.3943	4.6244	52.1248	55.1724
7	1.1768	-1.1503	0.4662	3.1201	2.4443	3.9192	-0.0586	0.1306	0.0881	0.1349	-0.0718	0.1915	0.0898	0.135	0.2956	0.178	-0.0545	-0.0345	0.1999	0.0122	0.311	-11.9858	39.8972	36.673
8	2.0208	0.3878	-1.287	1.5564	0.0227	3.259	-0.1307	-0.027	-0.0427	-0.0482	0.0008	0.2026	-0.1395	-0.1035	0.0045	0.1701	0.0193	-0.027	0.1816	0.0192	0.2902	-5.9775	34.4647	40.9455
9	6.3717	-3.0217	-0.2341	5.0033	-0.0134	3.4333	0.0143	-0.743	-0.1111	0.2208	0.0999	0.2276	-0.3169	-0.2029	-0.0926	0.2055	-0.0381	-0.0199	0.1737	-0.0026	0.1956	-14.0629	37.2056	46.9096
10	3.2232	-0.2692	-0.0948	2.1151	-1.1132	2.7995	0.0112	-0.0568	0.1391	-0.0429	-0.0788	-0.1671	-0.0817	0.3031	0.0581	0.2606	-0.0153	0.0373	0.1847	0.0282	0.2428	-13.1376	13.6517	5.7952
11	0.9645	-0.0883	0.2508	1.6007	0.4068	1.7126	0.1206	-0.1474	0.1475	-0.7223	-0.0296	-0.6374	-0.0016	0.1788	0.0088	0.1756	-0.0261	0.0924	0.2411	0.0498	0.2721	-13.8544	4.3135	21.6318
12	4.2514	0.3266	0.9203	2.8982	-2.4245	5.2777	-0.0858	-0.4573	0.2497	-0.0961	-0.4657	-0.6608	-0.8559	0.56	0.4512	0.3235	0.0094	0.0935	0.5065	-0.0374	0.7015	3.0938	0.0852	19.0882
13	0.8258	-0.4513	0.1467	2.3845	-0.9817	1.4773	-0.0178	0.1817	-0.2015	-0.1552	-0.0629	-0.003	0.1907	0.16	0.0615	0.2087	-0.0042	0.0255	0.2065	-0.0577	0.1734	-22.5691	-3.2401	19.6714
14	2.2233	0.3723	-0.6735	0.4826	0.4231	2.9112	-0.0027	0.1124	0.0306	0.3397	-0.181	-0.0815	0.0416	-0.0431	0.1135	0.2438	-0.039	0.0275	0.1444	0.0095	0.2947	-44.0888	24.7083	40.7405
15	5.4669	0.6263	-2.1847	1.9782	-1.255	5.3981	-0.02	0.2136	-0.2678	0.0518	0.0701	0.1897	0.3218	-0.2591	-0.0655	0.1905	-0.0406	-0.0701	0.1379	-0.0224	0.344	-46.7184	21.4959	29.794
16	1.1613	-0.2462	-1.3845	1.3692	-0.1185	1.9894	-0.0323	-0.2221	-0.2059	0.3098	-0.1003	0.1216	0.4332	-0.1964	0.1105	0.2344	-0.1048	0.0126	0.2487	-0.0003	0.3654	-32.3665	10.8846	47.5142
17	2.4525	-0.1822	1.3312	1.0529	0.091	1.6546	0.0087	-0.0549	-0.0654	0.1835	-0.0927	-0.1864	0.0392	0.0045	0.1081	0.1562	-0.0601	-0.0223	0.1951	0.0076	0.2513	-22.3711	22.8895	40.1279

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 130 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 131 through 255 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 3 through 51 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 52 through 92 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 93 through 130 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 131 through 154 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 155 through 185 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 186 through 226 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 227 through 252 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 4 through 92 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 93 through 127 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 128 through 147 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 148 through 255 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 4 through 51 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 52 through 92 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 93 through 162 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 163 through 254 )

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